Yesterday's violence in Cairo marks an ominous development in the story of Egypt's unfinished revolution. It is very bad news for several reasons. First, it demonstrates more starkly than ever the dubious role being played by the army. Eyewitness reports are clear that it was firing by the army, followed by the repeated crushing of unarmed demonstrators by an armoured car, that turned a peaceful demonstration for justice into a violent altercation that left 24 people dead. Twitter and Facebook networks are alive with conspiracy theorists speculating whether this is the army looking for excuses to delay the elections, or just clumsy crowd control by heavy-handed officers, but it marks a more direct face-off between army and demonstrators than we have seen for several months.

More specifically, the violence is very bad news for Egypt's beleaguered Coptic minority – the ancient Christian community that makes up between 10 and 15% of a population of 82 million, and is by far the largest Christian community in the region. The Copts stand to lose more than any other group in Egypt's current drift following the fall of an unpopular autocracy, and now face an uncertain future with a wide spectrum of possible outcomes, from a liberal democracy to an Islamic republic, or most likely of all, a continuation of army rule with different window-dressing.

That sectarian violence was likely to follow the end of Mubarak's regime was something that the Copts have been fearing for decades. Three years ago I attended some workshops organised by the Coptic newspaper editor Youssef Sidhom, intended to prepare his people for the rise of the Muslim Brotherhood, something many Copts believed was inevitable. Sidhom, editor of Watani, Egypt's leading Coptic newspaper, believed that dialogue between the two faiths was a pressing necessity and that the Copts would have to learn to live with the Islamists and reach an accommodation with a political grouping they have long feared.: "After the success of the Muslim Brothers in the elections we can no longer ignore them," he told me in 2008. "We need to enter into dialogue, to clarify their policies towards us, and end mutual mistrust."

The Copts have long suffered petty discrimination. But the revival of the Islamists over the last few years made the Copts' position more uneasy, and their prospects more uncertain, than they had been for centuries. Throughout the 1990s the Copts, especially in upper Egypt, were targeted by the Islamist guerrillas of the Gama'a Islamiyya. Since then, the Gama'a have renounced violence, and the Islamists concentrated on reaching power through the ballot box, something the Mubarak regime's passive policy towards Salafism encouraged. The Copts reacted by retreating ever deeper into a sectarian laager, further polarising the country. A generation ago, most Egyptians chose names for their children which could be either Christian or Muslim, such as Karim or Adel. Now they tend to give their children names such Mohammed or Girgis (George) that immediately define their sectarian affiliation. Likewise, the near-universal adoption of the hijab by Muslim women has left Coptic women exposed and sometimes subject to threats and abuse. In the face of growing polarisation and discrimination, the Copts have tended to form their own schools and social clubs, keeping their distance from the Muslim majority. This is something the Coptic clergy – every bit as conservative as their Muslim counterparts – have often encouraged.

At the same time, the Copts have seen their political influence slowly diminish: under Mubarak's last government there was still one Coptic provincial governor and two Coptic ministers. But in contrast to the situation at the time of Nasser and Sadat, no senior policemen are Copts, nor judges, nor university vice chancellors, nor military generals.

Yet if the Copts faced a certain amount of institutional discrimination, Mubarak was himself largely sympathetic to the community, and he made some significant gestures such making Christmas a national holiday and freeing up the rules on building new churches. Certainly, the Copts were well aware that things could get much worse for them.

Initially, the Tahrir Square demonstrations were a model of sectarian amity, with Muslim and Christian demonstrators protecting each other from the violence of the police and the regime's thugs. But in the growing uncertainty and violence that followed the fall of Mubarak, a spate of anti-Coptic riots of growing violence broke out in both Cairo and Alexandria which the army did very little to stop. In March a small clash in a Cairo suburb ended with the army sending in a Salafist sheikh to bring about reconciliation. In May, churches were attacked by Salafist mobs in the Cairo suburb of Imbaba, after rumours spread that a Muslim woman had been kidnapped by Copts, and Salafists called on Twitter for their supporters to mass "and free a Muslim sister". The army looked on as the churches burned, encouraging radicals to take the law into their own hands elsewhere. Yesterday the army-controlled media went a step further, encouraging patriotic citizens to defend the beleaguered army against what it described as "a Christian mob".

The dilemma and fears of the Copts mirror that of Christian minorities across the Middle East. Just as the elderly Coptic Pope Shenoudah supported Mubarak right up until the moment of his fall, whatever individual Copts were doing in Tahrir Square, so the churches in Syria are still publicly supporting the Asad regime, even if many Christian activists are at the forefront of the opposition.

At the back of their minds, the Christian hierarchies are aware of the devastation of the Iraqi Christian community after the fall of Saddam, when over half the Christian population – some 400,000 people – were forced to leave the country in a wave of Islamist pogroms. The Arab spring, it is widely feared, could yet mark the onset of the final Christian winter for the forgotten faithful of the Middle East. Only elections and the advent of sympathetic and stable democratic governments across the region is likely to allay such fears. Sadly, at the moment this outcome seems less likely with every passing day.